A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trn L-F and mat K sequences

Abstract.: The orchid subfamily Apostasioideae consists of two genera, Apostasia and Neuwiedia. To study the position of Apostasioideae within Orchidaceae and their intra- and intergeneric relationships, a molecular phylogenetic analysis has been conducted on the nuclear ITS region and the two plastid DNA regions trnL-F intron and matK. The two genera traditionally ascribed to Apostasioideae are each monophyletic. In Apostasia, A. nuda, with two stamens and no staminode, is sister to a clade comprising three species characterised by two stamens and one staminode. Within Neuwiedia, maximum parsimony analyses place N. zollingeri as sister to the clade formed by N. borneensis and N. veratrifolia. A family-wide phylogenetic analysis of matK sequences representing all proposed subfamilies of Orchidaceae produced five moderately to well-supported clades. One of these clades, Apostasioideae, is sister to the clade formed by Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae. High transition-transversion ratio and the absence of stop codons in the individual sequences suggest that matK is at the transition from a possibly functional gene to a pseudogene in Apostasioideae, contrary to what is found in some other groups of Orchidacea

A phylogenetic analysis of Apostasioideae (Orchidaceae) based on ITS, trn L-F and mat K sequences

The orchid subfamily Apostasioideae consists of two genera, Apostasia and Neuwiedia . To study the position of Apostasioideae within Orchidaceae and their intra- and intergeneric relationships, a molecular phylogenetic analysis has been conducted on the nuclear ITS region and the two plastid DNA regions trn L-F intron and mat K. The two genera traditionally ascribed to Apostasioideae are each monophyletic. In Apostasia , A. nuda , with two stamens and no staminode, is sister to a clade comprising three species characterised by two stamens and one staminode. Within Neuwiedia , maximum parsimony analyses place N. zollingeri as sister to the clade formed by N. borneensis and N. veratrifolia . A family-wide phylogenetic analysis of mat K sequences representing all proposed subfamilies of Orchidaceae produced five moderately to well-supported clades. One of these clades, Apostasioideae, is sister to the clade formed by Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae. High transition-transversion ratio and the absence of stop codons in the individual sequences suggest that mat K is at the transition from a possibly functional gene to a pseudogene in Apostasioideae, contrary to what is found in some other groups of Orchidaceae.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41641/1/606_2004_Article_133.pd

Structure and Development of Flowers and Inflorescences in Burmannia (Burmanniaceae, Dioscoreales)

Species of the genus Burmannia possess distinctive and highly elaborated flowers with prominent floral tubes that often bear large longitudinal wings. Complicated floral structure of Burmannia hampers understanding its floral evolutionary morphology and biology of the genus. In addition, information on structural features believed to be taxonomically important is lacking for some species. Here we provide an investigation of flowers and inflorescences of Burmannia based on a comprehensive sampling that included eight species with various lifestyles (autotrophic, partially mycoheterotrophic and mycoheterotrophic). We describe the diversity of inflorescence architecture in the genus: a basic (most likely, ancestral) inflorescence type is a thyrsoid comprising two cincinni, which is transformed into a botryoid in some species via reduction of the lateral cymes to single flowers. Burmannia oblonga differs from all the other studied species in having an adaxial (vs. transversal) floral prophyll. For the first time, we describe in detail early floral development in Burmannia. We report presence of the inner tepal lobes in B. oblonga, a species with reportedly absent inner tepals; the growth of the inner tepal lobes is arrested after the middle stage of floral development of this species, and therefore they are undetectable in a mature flower. Floral vasculature in Burmannia varies to reflect the variation of the size of the inner tepal lobes; in B. oblonga with the most reduced inner tepals their vascular supply is completely lost. The gynoecium consists of synascidiate, symplicate, and asymplicate zones. The symplicate zone is secondarily trilocular (except for its distal portion in some of the species) without visible traces of postgenital fusion, which prevented earlier researchers to correctly identify the zones within a definitive ovary. The placentas occupy the entire symplicate zone and a short distal portion of the synascidiate zone. Finally, we revealed an unexpected diversity of stamen-style interactions in Burmannia. In all species studied, the stamens are tightly arranged around the common style to occlude the flower entrance. However, in some species the stamens are free from the common style, whereas in the others the stamen connectives are postgenitally fused with the common style, which results in formation of a gynostegium

Sinocurculigo, a New Genus of Hypoxidaceae from China Based on Molecular and Morphological Evidence

, with eight species are distributed in China. Recently, we have found a hypoxid-like plant in China that is quite different in floral structure from any of the three genera and even of the known taxa in Hypoxidaceae. regions of 59 taxa in Hypoxidaceae and its alliance. Findings of the molecular investigation is consistent with those of the morphological analysis.

A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae)

Background: Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. Results: Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. Conclusions: The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological gradients in East Africa and South Africa appear to have resulted in more advanced allopatric speciation there

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple–sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple–sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are unable to accurately differentiate between highly similar sequences and are not designed to cope with hierarchic phylogenetic relationships or within taxon variability. Here, I present a novel alignment–free sequence identification algorithm–BRONX–that accounts for observed within taxon variability and hierarchic relationships among taxa. BRONX identifies short variable segments and corresponding invariant flanking regions in reference sequences. These flanking regions are used to score variable regions in the query sequence without the production of a global multiple–sequence alignment. By incorporating observed within taxon variability into the scoring procedure, misidentifications arising from shared alleles/haplotypes are minimized. An explicit treatment of more inclusive terminals allows for separate identifications to be made for each taxonomic level and/or for user–defined terminals. BRONX performs better than all other methods when there is imperfect overlap between query and reference sequences (e.g. mini–barcode queries against a full–length barcode database). BRONX consistently produced better identifications at the genus–level for all query types

Molecular phylogeny of Aerides (Orchidaceae) based on one nuclear and two plastid markers: a step in understanding the evolution of the Aeridinae

Phylogenetic relationships of the orchid genus Aerides (Epidendroideae, Vandeae, Aeridinae) from Southeast Asia were inferred from DNA sequences of one nuclear (nrITS) and two plastid (matK, trnL-trnL-F) regions of 48 taxa (21 Aerides, 25 other Aeridinae, 2 outgroup). Analyses of the combined datasets with parsimony, maximum likelihood and Bayesian methods revealed that Aerides is monophyletic and consists of three well-supported subclades which are only partly in accordance with previous sectional delimitations based on floral characters. The two different flower types in Aerides (hidden versus open spur entrance) seem to have evolved at least twice in geographically distinct areas. The phylogeny presented here is yet another example in Orchidaceae where floral morphology cannot be relied on to reconstruct phylogenetic history but rather is the result of pollinator-driven selection. The Aerides subclades are characterized by three different length classes of the mutation-rich P8 region in the trnL intron. To our knowledge, this is the first time that the P8 region was studied in orchids. The matK gene has been assumed to be a pseudogene in orchids due to occasional occurrence of frameshift indels, low transition/transversion (ts:tv) ratios and low substitution rates at the 3rd codon position. However, matK does not appear to be a pseudogene in Aerides and a comparison with data from other angiosperms suggests that ts:tv ratios and low substitution rates have been overestimated as arguments for a pseudogene status of matK in orchids